Sorta similar to Xenonsurf, on the time controlled patrol missions I tend to park the boat in the 50 mile zone unless near a known shipping area then I'll move toward them and park the boat as close as possible while remaining within the patrol zone to run out the 48 hour clock, using TC in target poor areas.
After accepting a seek and destroy mission, I head towards the nearest shipping lanes then zigzag across them at low speed. Since the criteria is tonnage sunk in these missions, there is a great deal of latitude as to where the patrol is completed. Don't know if the game is designed this way, but have never been admonished nor penalized for really stretching the definition of the search area.
Good hunting!